The lung has been recognized as one of the main targets of infectious and non-infectious complications of human Immunodeficiency virus type 1 (HIV-1) infection. Despite the initiation of HAART, pulmonary complications of H1V-1/AIDS continue to be a major cause of morbidity and mortality in HIV-1-infected patients. Defects in innate and adaptive immune responses increase the risk for the development of pneumonias caused by both pathogenic and opportunistic microorganisms in HIV-1-infected individuals. Following pneumonia, these individuals experience a decrement In lung function, which is not observed in HIV-1-uninfected populations. It remains unknown whether the deterioration of lung function or the development of chronic lung disease in the setting of HIV-1 infection is related to immunodeficiency, alteration in the lung microbiome and the subsequent development of chronic lung inflammation. Through our funded Longitudinal Studies of HIV-Associated Lung Infections and Complications program, we initiated a systematic analysis of nef sequences evolution in the lung and periphery using high-throughput sequencing platforms. These studies revealed interesting patterns of HlV-1 nef variants that are associated with HIV-1-related pulmonary arterial hypertension, a non-infectious complication of chronic HIV-1. With the advent of more highly advanced high-throughput sequencing technology, we can generate data sets of sufficient quality and depth that will allow us to make inferences as to how changes in disease stage influence the lung microbiota and affect the development and progression of HIV-1-related acute and chronic lung complications. Utilizing the tremendous expertise in the fields of HIV-1 pathogenesis, lung immunology, computational biology and bioinformatics present at the University of Colorado, we hypothesize that the immunodeficiency associated with l-ilV-1 infection leads to a broadening of the lung microbiome and that the inflammatory response to increased microbiota and HIV-1 variants will result in non- infectious chronic lung complications such as pulmonary arterial hypertension (PAH). In specific aim 1, we will determine the alterations in the lung microbiome associated with the development of both primary and chronic HIV-1 infection as compared to seronegative healthy control subjects and whether these alterations can be mitigated by controlling HIV-1 viral replication with HAART. The second aim will evaluate differences in the lung microbiome between chronically infected HIV-1 subjects with and without the presence of PAH and the association between HIV-1 variants and immunological responses that may affect virus evolution and the microbiome. In specific aim 3, metagenomic studies will be performed to quantify the bacterial lineages, genes, and encoded functional properties identified in the lung of selected subjects with varying stages of HlV-1 infection. These studies will advance our understanding ofthe relationship between alterations in the microbiome, innate and adaptive immunity, and the development of chronic lung disease. RELEVANCE (See instructions): Identification of the lung microbiome in HIV-1-infected and -uninfected individuals will enable us to learn which microbes are present in the human lung in health and disease. This knowledge will enhance our understanding of the role of these microbes and the resultant adaptive and innate immune responses in the development of noninfectious lung complications of HlV-1 infection. Understanding the lung microbiome in health and in subjects infected with HIV-1 will hopefully lead to the identification of predictors of disease progression and therapeutic targets for translation into better preventive and treatment strategies.